Story:
In 2286,
Kirk and company wait in self-imposed exile onVulcan, monitoring
Spock's progress as he remembers his past. On
Earth, the Federation Council is urged by the
Klingon Ambassador to produce Kirk for trial for his actions against
the Klingons on the Genesis Planet.
Ambassador Sarek denies the request to permit Kirk's extradition
from Vulcan and defends Kirk before the Council. The council agrees, yet
demands Kirk return to Earth to face his violation of nine Starfleet
regulations. Caught between two different sides, Kirk finally decides to
take the
Klingon Bird-of-Prey to Earth to face the Council's charges. Spock,
still suffering slightly from his fal-tor-pan, decides he must accompany
his captain.
The crew arrives to find Earth in turmoil, threatened by a deep space
probe that has drained all power and is vaporizing the oceans, producing
a worldwide cloud cover which begins to block the sun. Because of the
enormous storms ravaging the entire planet, Starfleet warns all
approaching spacecraft to keep their distance.
Spock manages to identify the probe's unusual communication, which turns
out to be a transmission to long-extinct humpback whales. When the
probe's signal is not answered, it increases its output, causing more
clouds and even more storms. Kirk and crew, orbiting the doomed planet,
decide that the only way to save Earth is to time-travel back to the
twentieth century, when whales still existed, and return to the present
with a pair of the mammals. With any luck, then the probe's signal might
be answered and Earth spared.

The crew, still
piloting the Bird-of-Prey, use the slingshot effect to travel back
in time. They pick up whale songs emanating from the West Coast of
North America. They land the Klingon warbird in a San Francisco
park, where thanks to its cloaking device, the ship is concealed
from view. However, the time traveling damaged the ship's valuable
dilithium crystals. The small crew then splits up, with Uhura and
Chekov assigned to locate an atomic reactor for photons to recharge
the ship's power, and McCoy, Scotty and Sulu ordered to create a
tank in the cargo bay that will safely house a pair of whales.

Kirk and Spock, after a
humorous trip through twentieth century San Francisco, locate Dr.
Gillian Taylor and her mated pair of whales, George and Gracie. Due
to cut-backs at the Maritime Cetacean Institute, where the whales
are on exhibit, they are due to be released in the sea. Once there,
Taylor fears the pair will be in danger from whale hunters. When
Spock performs a Vulcan mind-meld with the whales, he learns that
Gracie is pregnant. Kirk tries to convince the doctor that he's from
the future and that Starfleet will take good care of her whales, but
Taylor is, understandably, incredulous.

Meanwhile, Chekov and
Uhura have located enough photons from a reactor to complete their
mission — from the U.S.S. Enterprise CVN 65 aircraft
carrier, no less. Scotty, however, can't beam both crew members back
at once. Faced with a decision, Chekov sends Uhura up with the
needed photon collector. Chekov is then captured and questioned by
FBI agents. The Russian escapes, is chased by Marines, and
eventually falls and ends up hospitalized, in critical condition.

McCoy and Scotty have
concurrently arranged a trade for a large piece of Plexiglas to
build a whale tank on board the Klingon ship.

Kirk finally is able to
convince Gillian Taylor to help him, first in retrieving Chekov,
then the whales. Joined by McCoy, the three pull off a wild rescue,
springing Chekov from the hospital. With twenty-third century
medical technology, McCoy is able to quickly repair Chekov's
otherwise fatal condition. Kirk says goodbye to Gillian, assuring
her that her whales will be safe and, what's more, will be saving
the entire planet in the future. At the last second of Kirk's
transport, she throws her arms around him, transporting herself to
ship along with the captain.

Using the radio
frequency provided by Gillian, the crew locate the whales, now at
sea. Just as they are about to transport George and Gracie on board
the Klingon ship, a whaler ship comes into view, threatening the two
mammals. The future of Earth at stake, the Bird-of-Prey valiantly
fights off the whaler and beams up the whales, along with tons of
water, to the prepared tank in their cargo bay.

Off the planet and en
route to the Sun for the time-traveling slingshot maneuver, Spock
makes his calculations and the ship is propelled to the twenty-third
century. Arriving at Earth, the ship is rendered powerless by the
probe and crash-lands in San Francisco Bay. Kirk then releases the
whales and they answer the probe. Apparently satisfied, the probe
retreats back into deep space once more.

With Earth safe and the
storms gone, Kirk and his crew are brought before the Federation
Council to be reprimanded for stealing and destroying the U.S.S.
Enterprise in the rescue of Spock. Although Kirk disobeyed
direct orders and violated numerous Federation laws, the Council
praises the Admiral and his crew for saving Earth. And even though
Kirk is "demoted" to Captain, he is given the only job he ever
wanted — the command of a starship. And the ship he is given? A new
U.S.S. Enterprise, registry NCC-1701-A.